Using Synthetic Biology and pClone Red for Authentic Research on Promoter Function:
Genetics (analyzing mutant promoters)
Todd T. Eckdahl and A. Malcolm Campbell
Golden Gate Assembly with pClone Red
On the day when Golden Gate Assembly is to be performed, prepare a master mix for the
students that includes BsaI, T4 DNA Ligase, and Ligase Buffer.
Directions for 8 Lab Groups, 4 in the morning and 4 in the afternoon
Anytime before lab, store -20° C
1) Aliquot J119137 (receiving plasmid) to 73 ng/ µL (make at least 21 µL volume)
2) Aliquot J04450 (+ control) to 50 ng/ µL (make at least 10 µL volume)
3) Put 1 µL of J04450 into 9 tubes so that every group gets one tube (label with + (plus) on lid
for positive control). This will be used for the positive control transformation near the end of the
lab.
4) GGA Mixture contains these ingredients that can be made in advance (stored at -20° C):

10 µL J119137 (73 ng/µL)

60 µL water

10 µL 10X ligation buffer (included with Promega #M1804)

10 µL 500 mM potassium acetate (make stock solution at your institution)
Make two tubes with the volumes listed above. Label one tube AM and one tube PM for the two
lab sections. Each tube is enough for 4 groups, with each group using 2 tubes, plus a spare.
Day of the lab
5) Just before the lab, thaw one of the GGA Mixture tubes and add the following:

5 µL BsaI HF (New England BioLabs, #R3535L)

5 µL T4 DNA ligase (New England BioLabs, #M0202S)
6) For each lab section, mix the ingredients and aliquot 9 µL into 4 tubes (that fits your
thermocycler machine) so that each group gets two tubes, plus one spare. Lab one P for
(promoter) and one - (minus for negative control).
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7) Students will pipet 1 µL of their cooled and diluted oligos into the P tube and 1 µL of water
into the – (minus) tube. These tubes are placed into the thermocycler to perform GGA. The
thermal profile is 20 cycles of 1 minute at 37° C and 1 minute at 16° C, followed by one cycle of
15 minutes at 37° C, and a final hold at room temp. The + (plus) tube is only used for
transformation, so no GGA is required.
Students performed GGA reactions in a total volume of 10 µL containing 6 µL H2O, 1 µL
10X T4 DNA Ligase Buffer (included with order of ligase as 300mM Tris-HCl (pH 7.8 at 25°C),
100 mM MgCl2, 100 mM DTT and 10 mM ATP), 1 µL of 40 nM pClone Red, 1 µL of 40 nM
annealed promoter oligonucleotides, 0.5 µL HF (high fidelity; New England BioLabs) BsaI (10
units), 0.5 µL T4 DNA Ligase (New England BioLabs; 50 Weiss units). For each lab group, we
prepared a 8 µL master mix containing all of the components except the annealed
oligonucleotides and the pClone destination plasmid before class and stored it in the refrigerator
until needed later in the day. Students mixed the master mix, annealed oligos and pClone
destination plasmid. They placed their GGA reactions in a thermal cycler set for 20 cycles of 1
minute at 37° C followed by 1 minute at 16°C. The 37°C temperature favors digestion by BsaIHF while the 16°C favors ligation by T4 DNA ligase. GGA terminates with a 15 minute
incubation at 37° C to cleave any remaining BsaI sites. Students also performed a negative
control GGA in which the annealed oligos are replaced by water.
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